The Parisian club has now secured the prestigious trophy on fourteen different occasions.
Paris Saint-Germain needed a dramatic leveler followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup victory.
The European champions appeared to be sailing towards a comfortable win in the showdown between the French league champions and the Coupe de France holders after the French winger found the scoring early on.
However, Marseille fired twice late to seize a surprise lead. Initially, the English forward converted from the spot-kick, before the defender inadvertently turned the ball into his own net for an own goal.
In a breathtaking turn of events, the Portuguese striker grabbed a crucial equaliser in the final moments to force the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping decisive kicks from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to complete a 4-1 penalty win.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now won this competition for the twelfth time in the last 13 years.